Taxonomic profiling of bacterial and archaeal communities from saliva, stool, and CapScan-sampled gut metagenomes

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Subject: AL

Envivo Bio, Inc.; Confidential

1.1 Overview of microbial community composition

Figure 1 is an interactive figure showing the microbial community composition in each collected sample. Here, each color and shade corresponds to a different genus. For reference, domestic dogs (Canis familiaris) and gray wolves (Canis lupus) are different species that belong to the same genus (Canis).

You can interact with this figure by:

• Hovering the cursor over a color in the stacked bar to see the taxonomic identity, sample type, and relative abundance corresponding to that color and bar
• Clicking and dragging the cursor over a portion of the figure to zoom
• Single-clicking a genus’s name in the legend to remove that genus from the figure
• Double-clicking (very quickly) a genus’s name in the legend to only show that genus

Figure 1: Microbial community composition of collected saliva, stool, and CapScan samples. CapScan samples are ordered from proximal to distal intestine (i.e., increasing distance from mouth). Taxonomic composition is reported at the genus rank. Genera present at <1% relative abundance across all samples are reported as “Other genera”. Note: Blue = Firmicutes; Yellow = Actinomycetes; Green = Bacteroidetes; Red = Proteobacteria; Purple = all other phyla. Shades of the same color (except purple) correspond to different genera from the same phylum.

1.2 High-resolution snapshot of community composition

Figure 2 is an interactive figure showing the microbial community composition at higher taxononomic resolution. Here, each row corresponds to a unique microbe.

You can interact with this figure by:

• Hovering the cursor over a cell to see that microbe’s genus and species (and strain when available), relative abundance, and full taxonomic classification
• Clicking and dragging the cursor over a portion of the figure to zoom

Figure 2: Heat map showing relative abundance of microbes in each sample (N = 266 total identified). Each row corresponds to a unique microbe and each column corresponds to an individual sample. Note the relative abundance colorscale is in log units.

1.3 Notable microbes detected

• Bacteroides:
  • Production of proteases from a few different species linked to gut inflammation, such as Bacteroides vulgatus (Mills et al., 2022) and Bacteroides fragilis (Wu et al., 2009)
  • Note: Genera Bacteroides and Phocaeicola are very closely related, with a recent reclassification of some Bacteroides as Phocaeicola (García-López et al., 2019). There are conflicting taxonomic assignments in this dataset (e.g., genus identified as Phocaeicola but strain listed under Bacteroides) – to help interpretation, regard Bacteroides and Phocaeicola as one genus.
    
    

1.4 References

García-López, M., Meier-Kolthoff, J.P., Tindall, B.J., Gronow, S., Woyke, T., Kyrpides, N.C., et al. (2019) Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes. Front Microbiol 10: https://doi.org/10.3389/fmicb.2019.02083.

Mills, R.H., Dulai, P.S., Vázquez-Baeza, Y., Sauceda, C., Daniel, N., Gerner, R.R., et al. (2022) Multi-omics analyses of the ulcerative colitis gut microbiome link Bacteroides vulgatus proteases with disease severity. Nat Microbiol 7: 262–276.

Wu, S., Rhee, K.J., Albesiano, E., Rabizadeh, S., Wu, X., Yen, H.R., et al. (2009) A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses. Nat Med 15: 1016–1022.